MolNFT v1 · #155548 · protein + DNA
Crystal structure of PA4674 in complex with its operator DNA (18BP) from pseudomonas aeruginosa
6LB3 · Hth CRO/C1-type domain-containing protein: “Crystal structure of PA4674 in complex with its operator DNA (18BP) from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.77). MolNFT v1 #155548…
- PDB
- 6LB3
- Type
- protein + DNA
- Length
- 821 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth CRO/C1-type domain-containing protein; DNA (5'…
- UniProt
- Q9HVC1
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 11 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth CRO/C1-type domain-containing protein | protein | 91 | 70% helix, 0% strand | Q9HVC1 |
| B, C | Hth CRO/C1-type domain-containing protein | protein | 93 | 66% helix, 0% strand | Q9HVC1 |
| D | Hth CRO/C1-type domain-containing protein | protein | 92 | 64% helix, 0% strand | Q9HVC1 |
| E | Hth CRO/C1-type domain-containing protein | protein | 90 | 59% helix, 0% strand | Q9HVC1 |
| F | Hth CRO/C1-type domain-containing protein | protein | 93 | 65% helix, 0% strand | Q9HVC1 |
| G | Hth CRO/C1-type domain-containing protein | protein | 88 | 59% helix, 0% strand | Q9HVC1 |
| H | Hth CRO/C1-type domain-containing protein | protein | 95 | 62% helix, 0% strand | Q9HVC1 |
| I, K | DNA (5'- D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3') | dna | 18 | — | — |
| J, L | DNA (5'- D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3') | dna | 18 | — | — |
| M | DNA (5'- D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3') | dna | 7 | — | — |
| N | DNA (5'- D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3') | dna | 7 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.77 | 0.81 | 56 | empty |
| 2 | 751 | 0.76 | 0.81 | 56 | empty |
| 3 | 556 | 0.67 | 0.78 | 37 | empty |
| 4 | 512 | 0.66 | 0.78 | 32 | empty |
| 5 | 134 | 0.47 | 0.78 | 23 | empty |
Interfaces
27 interfaces between chains.
- A–B · 1484 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1474 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1441 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1417 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 794 Ų buried · 74 hydrogen bonds · nucleic-nucleic
Compared structures
- 6LB3 · Crystal structure of PA4674 in complex with its operator DNA (18bp) from Pseudomonas… · the same entry in another collection · chain I against I, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9HVC1
- Elsewhere: RCSB PDB 6LB3 · PDBe 6LB3 · UniProt Q9HVC1
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